MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 6712 to 6761 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
420	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]	Squared	Subtracted	1	32192.8	37967.1	5774.3
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Measured	Divided		10235.2	11830.8	1.15589
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted		0	6.9282	7.14143	1.03078
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Measured	Subtracted		548.5	527.5	21
	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]			1	5942.49	6853.15	910.66
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Squared	Divided	0	2268.24	2378.75	1.04872
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]		Subtracted		1.22698	5.39669	4.16971
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Rooted			18.8643	18.2434	0.6209
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Measured	Divided		18889	19496	1.03214
421	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Ranked			11186	10866.3	1.02942
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Rooted		1	50.4666	45.9317	1.09873
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Squared			36933	44953.6	1.21717
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		Subtracted	0	4.16226	0.02001	4.14225
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]		Divided		2892.28	2758.62	1.04845
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Measured	Subtracted	1	6739.43	7644.55	905.12
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Squared			32189.9	37963.6	5773.7
	importin 4. [refseq;acc:nm_024658]	Measured	Divided	0	491.926	476.639	1.03207
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]		Subtracted		613.385	634.192	20.807
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Ranked			10854.8	10537.9	316.9
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Rooted	Divided		6.9282	7.14143	1.03078
	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	Ranked	Subtracted	1	238.704	255.68	16.976
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	Rooted		0	48.2804	48.8876	0.6072
	thrombospondin 3 precursor. [swissprot;acc:p49746]			1	51.6132	45.8422	5.771
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Ranked	Divided		223.202	205.9	1.08403
	vav-2 protein. [swissprot;acc:p52735]	Measured			6660.02	7697.78	1.15582
422	60s ribosomal protein l5. [swissprot;acc:p46777]	Rooted			50.4641	45.9293	1.09873
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Squared		0	9431	9001.76	1.04768
	block 23. [sptrembl;acc:q8nhw5]	Rooted	Subtracted		22.6329	22.0536	0.5793
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Measured		1	460	1365	905
	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	Squared	Divided		25860	31475.4	1.21715
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Ranked		0	12581.7	12224.2	1.02925
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Squared	Subtracted	1	32188.2	37961.6	5773.4
	kappa b-ras 1. [refseq;acc:nm_020345]	Measured	Divided	0	1153.15	1117.36	1.03203
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Squared	Subtracted		6.13515	2.13609	3.99906
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Rooted	Divided		6.9282	7.14143	1.03078
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Measured		1	5206.9	6010.04	1.15425
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Rooted	Subtracted		80.4069	86.1018	5.6949
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Measured		0	178.955	199.751	20.796
	ras-related protein rab-37. [swissprot;acc:q96ax2]	Ranked	Divided	1	240.287	260.193	1.08284
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]		Subtracted		238.704	255.68	16.976
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]			0	3464	3778	314
423	40s ribosomal protein s26. [swissprot;acc:p02383]	Squared			8.80383	5.24885	3.55498
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Ranked			12318.7	12631.5	312.8
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Squared	Divided		8975.38	9403.03	1.04765
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Ranked			5905	6073	1.02845
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Measured	Subtracted		1562.36	1541.69	20.67
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Rooted	Divided	1	50.4663	45.9313	1.09873
	fibrillin 3. [refseq;acc:nm_032447]	Measured		0	14246	13809	1.03165
	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]		Subtracted	1	6739.61	7644.58	904.97
		Squared			32187.7	37961	5773.3

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.